Can I put a small resolution scene on top of a large scene in one go?
In order to have 2 scenes at different resolutions while rendered together without any saving render results to file you will need to setup 2 scenes (in this case for saving resources it would be useful to create linked copy of the scene; make sure to make camera single-user so it to be scene independent). Use Render Layers nodes with scenes selected and make transparent or crop image of the scene at the lower resolution; after that overlay scenes as usual.

The Crop node will allow to make all the pixels of the image at lower resolution become transparent so that the background image will be visible as expected, without any stretching:


  Crop Image Size
      When enabled, the image size is cropped to the specified region. When disabled, the image remains the same size, and uncropped areas become transparent pixels.  
  
  Crop node in manual


Once scene at lower resolution is made transparent in empty areas, most likely you would like to translate it by X or Y axes with Translate node to see the background image as desired.



This can also work with Crop Image Size enabled with the only difference that image of the scene at lower resolution will be cropped and not made transparent in empty areas. 

Note that if one of the scenes was changed, it's possible to rerender only it and see the final overlayed result once compositing nodes process it.